I have these kind of files:
file6543_015.bam
subreadset_15.xml
file6543_024.bam
subreadset_24.xml
file6543_027.bam
subreadset_27.xml
I would like to run something like this:
for i in *bam && l in *xml
do
my_script $i $l > output_file
done
Because in my command the first bam file goes with the first xml file. For each combination bam/xml, that command will give a specific output file.
Like this, using bash arrays:
bam=( *.bam )
xml=( *.xml )
for ((i=0; i<${#bam[#]}; i++)); do
my_script "${bam[i]}" "${xml[i]}"
done
Assuming you have way to uniquely name your output_file for each specific output,
here is one way:
#!/bin/bash
ls file*.bam | while read i
do
CMD=`echo -n "my_script $i "`
CMD="$CMD `echo $i | sed -e 's/file.*_0/subreadset_/' -e 's/.bam/.xml/'`"
$CMD >> output_file
done
Related
I have a textfile called log.txt, and it logs the file name and the path it was gotten from. so something like this
2.txt
/home/test/etc/2.txt
basically the file name and its previous location. I want to use grep to grab the file directory save it as a variable and move the file back to its original location.
for var in "$#"
do
if grep "$var" log.txt
then
# code if found
else
# code if not found
fi
this just prints out to the console the 2.txt and its directory since the directory has 2.txt in it.
thanks.
Maybe flip the logic to make it more efficient?
f=''
while read prev
do case "$prev" in
*/*) f="${prev##*/}"; continue;; # remember the name
*) [[ -e "$f" ]] && mv "$f" "$prev";;
done < log.txt
That walks through all the files in the log and if they exist locally, move them back. Should be functionally the same without a grep per file.
If the name is always the same then why save it in the log at all?
If it is, then
while read prev
do f="${prev##*/}" # strip the path info
[[ -e "$f" ]] && mv "$f" "$prev"
done < <( grep / log.txt )
Having the file names on the same line would significantly simplify your script. But maybe try something like
# Convert from command-line arguments to lines
printf '%s\n' "$#" |
# Pair up with entries in file
awk 'NR==FNR { f[$0]; next }
FNR%2 { if ($0 in f) p=$0; else p=""; next }
p { print "mv \"" p "\" \"" $0 "\"" }' - log.txt |
sh
Test it by replacing sh with cat and see what you get. If it looks correct, switch back.
Briefly, something similar could perhaps be pulled off with printf '%s\n' "$#" | grep -A 1 -Fxf - log.txt but you end up having to parse the output to pair up the output lines anyway.
Another solution:
for f in `grep -v "/" log.txt`; do
grep "/$f" log.txt | xargs -I{} cp $f {}
done
grep -q (for "quiet") stops the output
I would like to run commands such as "history" or "!23" off of a pipe.
How might I achieve this?
Why does the following command not work?
echo "history" | xargs eval $1
To answer (2) first:
history and eval are both bash builtins. So xargs cannot run either of them.
xargs does not use $1 arguments. man xargs for the correct syntax.
For (1), it doesn't really make much sense to do what you are attempting because shell history is not likely to be synchronised between invocations, but you could try something like:
{ echo 'history'; echo '!23'; } | bash -i
or:
{ echo 'history'; echo '!23'; } | while read -r cmd; do eval "$cmd"; done
Note that pipelines run inside subshells. Environment changes are not retained:
x=1; echo "x=2" | while read -r cmd; do eval "$cmd"; done; echo "$x"
You can try like this
First redirect the history commands to a file (cut out the line numbers)
history | cut -c 8- > cmd.txt
Now Create this script hcmd.sh(Referred to this Read a file line by line assigning the value to a variable)
#!/bin/bash
while IFS='' read -r line || [[ -n "$line" ]]; do
echo "Text read from file: $line"
$line
done < "cmd.txt"
Run it like this
./hcmd.sh
I have been working in bash, and need to create a string argument. bash is a newish for me, to the point that I dont know how to build a string in bash from a list.
// foo.txt is a list of abs file names.
/foo/bar/a.txt
/foo/bar/b.txt
/delta/test/b.txt
should turn into: a.txt,b.txt,b.txt
OR: /foo/bar/a.txt,/foo/bar/b.txt,/delta/test/b.txt
code
s = ""
for file in $(cat foo.txt);
do
#what goes here? s += $file ?
done
myShellScript --script $s
I figure there was an easy way to do this.
with for loop:
for file in $(cat foo.txt);do echo -n "$file",;done|sed 's/,$/\n/g'
with tr:
cat foo.txt|tr '\n' ','|sed 's/,$/\n/g'
only sed:
sed ':a;N;$!ba;s/\n/,/g' foo.txt
This seems to work:
#!/bin/bash
input="foo.txt"
while IFS= read -r var
do
basename $var >> tmp
done < "$input"
paste -d, -s tmp > result.txt
output: a.txt,b.txt,b.txt
basename gets you the file names you need and paste will put them in the order you seem to need.
The input field separator can be used with set to create split/join functionality:
# split the lines of foo.txt into positional parameters
IFS=$'\n'
set $(< foo.txt)
# join with commas
IFS=,
echo "$*"
For just the file names, add some sed:
IFS=$'\n'; set $(sed 's|.*/||' foo.txt); IFS=,; echo "$*"
I have a file of filenames, and I need to be able to get the size of these files using bash.
I have the following script which does that, but It prints the filename and the size on different lines, i'd prefer it to do it all on one line if possible.
#!/bin/sh
filename="$1"
while read -r line
do
name=$line
vars=(`echo $name | tr '.' ' '`)
echo $name
stat -x $name | grep Size: | awk '{ print $2 }'
done < "$filename"
I'd love to have it of the form:
filename: $size
How can I do this?
(I am using OSX hence the slightly odd version of stat.)
Pass -n to the echo to prevent a trailing newline from being added. So change
echo $name
to
echo -n $name
and to add the : separator between the file name and file size
echo -n ${name}": "
This should do the trick:
while read f
do
echo "${f} : $(stat -L -c %s ${f})"
done < "${filename}"
echo $name: $(stat -x $name | sed -n '/^Size:/s///p')
I want convert a column of data in a txt file to a row of a csv file using unix commands.
example:
ApplChk1,
ApplChk2,
v_baseLoanAmountTI,
v_plannedClosingDateField,
downPaymentTI,
this is a column which present in a txt file
I want output as follows in a csv file
ApplChk1,ApplChk2,v_baseLoanAmountTI,v_plannedClosingDateField,downPaymentTI,
Please let me know how to do it.
Thanks in advance
If that's a single column, which you want to convert to row, then there are many possibilities:
tr -d '\n' < filename ; echo # option 1 OR
xargs echo -n < filename ; echo # option 2 (This option however, will shrink spaces & eat quotes) OR
while read x; do echo -n "$x" ; done < filename; echo # option 3
Please let us know, how the input would look like, for multi-line case.
A funny pure bash solution (bash ≥ 4.1):
mapfile -t < file.txt; printf '%s' "${MAPFILE[#]}" $'\n'
Done!
for i in `< file.txt` ; do echo -n $i; done; echo ""
gives the output
ApplChk1,ApplChk2,v_baseLoanAmountTI,v_plannedClosingDateField,downPaymentTI,
To send output to a file:
{ for i in `< file.txt` ; do echo -n $i ; done; echo; } > out.csv
When I run it, this is what happens:
[jenny#jennys:tmp]$ more file.txt
ApplChk1,
ApplChk2,
v_baseLoanAmountTI,
v_plannedClosingDateField,
downPaymentTI,
[jenny#jenny:tmp]$ { for i in `< file.txt` ; do echo -n $i ; done; echo; } > out.csv
[jenny#jenny:tmp]$ more out.csv
ApplChk1,ApplChk2,v_baseLoanAmountTI,v_plannedClosingDateField,downPaymentTI,
perl -pe 's/\n//g' your_file
the above will output to stdout.
if you want to do it in place:
perl -pi -e 's/\n//g' your_file
You could use the Linux command sed to replace line \n breaks by commas , or space :
sed -z 's/\n/,/g' test.txt > test.csv
You could also add the -i option if you want to change file in-place :
sed -i -z 's/\n/,/g' test.txt